# List of top-scoring protein chains for t2k-100-30-alpha-scores hidden Markov model. # HMM and HMM E-value scores computed by SAM (c) 1992-2001 Regents of the University of California, Santa Cruz # Sequence Alignment and Modeling Software System # http://www.soe.ucsc.edu/research/compbio/sam.html # ----------------- Citations (SAM, SAM-T99, HMMs) -------------------- # R. Hughey, A. Krogh, Hidden Markov models for sequence analysis: # Extension and analysis of the basic method, CABIOS 12:95-107, 1996. # K. Karplus, C. Barrett, R. Hughey, Hidden Markov models for detecting # remote protein homologies, Bioinformatics 14(10):846-856, 1998. # A. Krogh et al., Hidden Markov models in computational biology: # Applications to protein modeling, JMB 235:1501-1531, Feb 1994. # # FSSP representative for each protein chain taken from FSSP: # ------------------Citations (FSSP) ----------------------------------- # L. Holm and C. Sander (1996) Mapping the protein universe. Science 273:595-602. # #SCOP domains found in each protein chain taken from SCOP: # ------------------Citations (SCOP) ----------------------------------- #Murzin A. G., Brenner S. E., Hubbard T., Chothia C. (1995). #SCOP: a structural classification of proteins database for the investigation of sequences and structures. #J. Mol. Biol. 247, 536-540. Sequence_ID Length Target_Evalue FSSP-rep SCOP_domain SCOP_suid 5S 5N 12S 6S 12S 10N 3lmmA 583 4.44e-05 1hh1A 143 5.46e-01 1gefA c.52.1.18 61036 1yzgA 179 7.59e-01 c.37.1.8 124276 2zo4A 317 7.87e-01 2qtfA 364 8.27e-01 1f6bA 198 8.53e-01 c.37.1.8 64986 2eo0A 147 9.17e-01 1mkyA 439 1.02e+00 c.37.1.8,c.37.1.8,d.52.5.1 79250,79251,79252 1ln1A 214 1.49e+00 d.129.3.2 74038 1kshA 186 1.72e+00 c.37.1.8 72914 2f1nA 262 2.29e+00 d.151.1.1 132782 1zj6A 187 2.48e+00 c.37.1.8 125145 3gokA 334 3.17e+00 1an7A 136 3.69e+00 1seiA d.140.1.1 41465 1o3yA 166 4.20e+00 c.37.1.8 86618 3cjiC 284 4.39e+00 1y7pA 223 4.47e+00 c.23.1.7,d.58.18.12 122708,122709 2oxgA 108 4.52e+00 1urjA 1136 4.65e+00 e.58.1.1 113410 2h17A 181 4.72e+00 1m2oB 190 4.91e+00 c.37.1.8 78485 2a5dA 175 5.00e+00 c.37.1.8 126172 2w83A 165 5.54e+00 1x9nA 688 5.61e+00 a.235.1.1,b.40.4.6,d.142.2.1 115002,115003,115004 1wgpA 137 5.99e+00 b.82.3.2 114619 1k20A 310 6.24e+00 c.107.1.1 68027 1cfyA 143 6.46e+00 1cof d.109.1.2 40858 1uptA 171 6.53e+00 c.37.1.8 99767 1wcuA 153 6.57e+00 1fa0A 537 6.88e+00 1fa0B d.58.16.1,a.160.1.1,d.218.1.3 39335,75837,75838 2hhpA 530 7.05e+00 a.160.1.1,d.218.1.3,d.58.16.1 136503,136504,136505 2q3xA 171 7.33e+00 2cxcA 144 7.33e+00 3a57A 165 8.28e+00 1hw7A 255 9.00e+00 1i7fA d.193.1.1 61297 2ifeA 100 9.19e+00 1tig d.68.1.1 39567 2jbwA 386 9.30e+00 c.69.1.41 147962 1wi1A 126 9.40e+00 b.55.1.1 114658 2q66A 525 9.48e+00 a.160.1.1,d.218.1.3,d.58.16.1 150057,150058,150059 1mvfD 82 9.52e+00 b.129.1.1 85143 1u55A 188 9.61e+00 d.278.1.1 107677 1v2bA 177 9.74e+00 d.107.1.2 108279 1ub4C 85 9.93e+00 b.129.1.1 88401 1qciA 262 1.02e+01 1qi7A d.165.1.1 42201 1ok8A 394 1.07e+01 b.1.18.4,f.10.1.1 93236,93237 3glaA 100 1.07e+01 1ib8A 164 1.09e+01 b.38.2.1,d.52.4.1 71168,71169 1ukvY 206 1.16e+01 c.37.1.8 107918 1yemA 179 1.16e+01 d.63.1.2 116646 3g7eA 203 1.20e+01 3fhrA 336 1.22e+01 1kobA 387 1.23e+01 1tkiA d.144.1.7 41640 2h57A 190 1.26e+01 3fucA 284 1.27e+01 1gycA 499 1.28e+01 b.6.1.3,b.6.1.3,b.6.1.3 70748,70749,70750 1ry9A 145 1.34e+01 d.198.1.1 98094 2hqyA 305 1.35e+01 d.108.1.4,d.108.1.4 147365,147366 3lahA 188 1.37e+01 3kg7A 293 1.38e+01 1bvoA 175 1.39e+01 1a3qA b.2.5.3 22457 2fm8A 135 1.44e+01 d.198.1.1 133767 2bcgY 206 1.45e+01 c.37.1.8 128285 1hdfA 102 1.51e+01 1ag4 b.11.1.1 23627 2gtdA 251 1.52e+01 c.55.1.13,c.55.1.13 135634,135635 2qm4A 235 1.55e+01 2hrgA 496 1.61e+01 2eisA 133 1.61e+01 2uubE 162 1.63e+01 d.14.1.1,d.50.1.2 139936,139937 3f10A 292 1.66e+01 2pqvA 154 1.67e+01 1oygA 447 1.70e+01 b.67.2.2 93726 2vqeE 162 1.70e+01 i.1.1.3 153429 2hlyA 207 1.71e+01 d.3.1.19 147310 3ckwA 304 1.71e+01 3kspA 129 1.73e+01 2i8dA 123 1.76e+01 d.198.4.1 147561 1fvrA 327 1.78e+01 d.144.1.7 60047 1o8uA 257 1.84e+01 c.14.1.3 81194 2r41A 110 1.85e+01 3silA 379 1.88e+01 b.68.1.1 27542 1i1nA 226 1.89e+01 c.66.1.7 71102 3encA 87 1.90e+01 1rypH 205 1.93e+01 d.153.1.4 41876 2qkmB 266 1.99e+01 3fdjA 278 2.02e+01 1rxyA 253 2.03e+01 c.56.2.1 98065 2bm0A 691 2.04e+01 b.43.3.1,c.37.1.8,d.14.1.1,d.58.11.1,d.58.11.1 128748,128749,128750,128751,128752 1r4aA 165 2.07e+01 c.37.1.8 96986 3ezjA 241 2.08e+01 2kptA 148 2.11e+01 2zjrG 174 2.12e+01 c.21.1.1 154560 3i0wA 290 2.17e+01 3k86A 185 2.18e+01 2qpzA 103 2.18e+01 1j1qA 261 2.18e+01 d.165.1.1 90768 1vlmA 219 2.22e+01 c.66.1.41 108836 1m2rA 327 2.26e+01 d.144.1.7 84760 2ze3A 275 2.27e+01 3l2nA 395 2.30e+01 2vvrA 149 2.31e+01 1y8cA 246 2.32e+01 c.66.1.43 116563 2fqxA 318 2.40e+01 3lqaG 332 2.41e+01 2oezA 247 2.42e+01 e.68.1.1 148758 1vkkA 154 2.48e+01 d.109.1.2 108669 1szoA 257 2.49e+01 c.14.1.3 106164 1vfgA 390 2.50e+01 a.173.1.1,d.218.1.4 108570,108571 2ggoA 401 2.54e+01 2ek0A 90 2.56e+01 1ds1A 324 2.57e+01 1drtA b.82.2.2 28127 1onqA 283 2.60e+01 b.1.1.2,d.19.1.1 93365,93366 2avtA 378 2.61e+01 2w5yA 192 2.64e+01 1zc1A 208 2.67e+01 3id2A 90 2.70e+01 2ch9A 131 2.71e+01 1ji6A 589 2.73e+01 b.18.1.3,b.77.2.1,f.1.3.1 63066,63067,63068 3lk41 286 2.75e+01 1xocA 520 2.75e+01 c.94.1.1 122201 2vu4A 273 2.77e+01 2isnA 364 2.77e+01 1n1tA 641 2.79e+01 b.29.1.15,b.68.1.1 79821,79822 3h5kA 261 2.86e+01 3c8nA 356 2.87e+01 3hx9A 124 2.87e+01 1hyvA 166 2.90e+01 1b9dA c.55.3.2 61424 1pmnA 364 2.93e+01 d.144.1.7 94907 1l0oA 150 2.95e+01 d.122.1.3 73403 3l3uA 163 2.96e+01 1fzqA 181 2.96e+01 1hurA c.37.1.8 32060 1iznA 286 2.97e+01 e.43.1.1 83847 1vr8A 142 3.00e+01 d.312.1.1 120445 2f57A 317 3.01e+01 1vmkA 277 3.03e+01 c.56.2.1 113680 1s5uA 138 3.04e+01 d.38.1.1 98573 1jpcA 109 3.09e+01 b.78.1.1 27986 1fjgE 162 3.10e+01 1pkp d.14.1.1,d.50.1.2 37553,38789 3bexA 249 3.12e+01 c.55.1.13,c.55.1.13 155198,155199 2fu5C 183 3.12e+01 c.37.1.8 134104 1vd6A 224 3.13e+01 c.1.18.3 119991 1kcxA 518 3.15e+01 b.92.1.3,c.1.9.6 90953,90954 3cngA 189 3.15e+01 3c0dA 119 3.18e+01 b.33.1.3 155819 1mz5A 638 3.22e+01 b.29.1.15,b.68.1.1 79679,79680 2fltA 149 3.24e+01 2gxfA 142 3.28e+01 d.17.4.22 147191 3cptB 131 3.29e+01 1bl3A 160 3.31e+01 1b9dA c.55.3.2 33655 1xtmA 175 3.35e+01 1pg4A 652 3.37e+01 e.23.1.1 88067 2b0vA 153 3.44e+01 d.113.1.1 127650 1hz6A 72 3.50e+01 2ptl d.15.7.1 61429 2i79A 172 3.52e+01 2z06A 252 3.52e+01 d.159.1.10 153906 2qdkA 252 3.52e+01 2i8aA 252 3.54e+01 1itg 166 3.55e+01 1b9dA 3f0zA 292 3.60e+01 3greA 437 3.63e+01 2gysA 419 3.72e+01 b.1.2.1,b.1.2.1,b.1.2.1,b.1.2.1 135865,135866,135867,135868 1v10A 521 3.72e+01 b.6.1.3,b.6.1.3,b.6.1.3 108224,108225,108226 2vv6A 119 3.75e+01 1wk2A 121 3.78e+01 b.122.1.5 114720 3bwuC 205 3.79e+01 b.1.11.1,b.7.2.1 155699,155700 2ca9A 148 3.79e+01 1th8A 145 3.80e+01 d.122.1.3 106908 1trbA 320 3.80e+01 c.3.1.5,c.3.1.5 30529,30530 2vouA 397 3.82e+01 c.3.1.2,d.16.1.2 153389,153390 3a6sA 129 3.85e+01 3e7eA 365 3.85e+01 3c5xA 402 3.86e+01 1jk8B 190 3.88e+01 1iakB b.1.1.2,d.19.1.1 63147,63148 3holA 509 3.89e+01 3efyA 195 3.89e+01 3k50A 403 3.96e+01 2dasA 62 3.96e+01 g.39.1.17 146476 3id3A 89 3.98e+01 2go8A 122 4.00e+01 d.58.4.5 147144 3ddoA 253 4.00e+01 1t4hA 290 4.02e+01 d.144.1.7 106420 3ga2A 246 4.02e+01 3divA 499 4.03e+01 2a5jA 191 4.06e+01 c.37.1.8 126175 2p5dA 147 4.09e+01 2w02A 620 4.09e+01 1hd7A 318 4.11e+01 1bix d.151.1.1 41780 1xm7A 195 4.16e+01 d.159.1.8 115473 2ux0A 143 4.26e+01 d.17.4.7 152231 3gzrA 146 4.28e+01 2ov7A 137 4.30e+01 3fruA 269 4.31e+01 1agdA b.1.1.2,d.19.1.1 20657,38150 2iorA 235 4.34e+01 3d79A 179 4.35e+01 1vraA 208 4.35e+01 2htaA 309 4.43e+01 2g5fA 450 4.46e+01 d.161.1.1 134654 1om1A 332 4.49e+01 d.144.1.7 93347 2cw2A 226 4.53e+01 1vetB 125 4.58e+01 d.110.7.1 108554 2ai6A 125 4.62e+01 d.322.1.1 126818 1s98A 107 4.64e+01 b.124.1.1 105377 2phpA 192 4.73e+01 c.74.1.2 149474 1vmeA 410 4.75e+01 c.23.5.1,d.157.1.3 108893,108894 1z57A 339 4.80e+01 2o3hA 285 4.80e+01 2qiyA 154 4.81e+01 d.17.4.2 150815 1rf6A 427 4.83e+01 d.68.2.2 97366 2eb0A 307 4.88e+01 2pmaA 146 4.88e+01 b.50.1.3 149657 1m5sA 297 4.89e+01 d.58.33.1,d.58.33.1 74511,74512 3ec6A 139 4.90e+01 2hrdA 253 4.92e+01 2a6tA 271 4.92e+01 a.242.1.1,d.113.1.7 126309,126310 3gnlA 244 4.92e+01 2qckA 167 4.95e+01 2wwxA 175 5.00e+01 3kw7A 502 5.01e+01 1a6aA 176 5.03e+01 1iakA b.1.1.2,d.19.1.1 21615,38189 2b5uA 551 5.03e+01 b.101.1.1,b.110.1.1,h.4.9.1 127906,127907,127908 1m65A 245 5.06e+01 c.6.3.1 84847 1vkdA 338 5.06e+01 b.67.2.4 108644 1f8fA 371 5.06e+01 b.35.1.2,c.2.1.1 83246,83247 3e29A 144 5.09e+01 1gtkA 313 5.09e+01 c.94.1.1,d.50.2.1 76346,76347 2i52A 121 5.10e+01 d.316.1.1 137055 1hkxA 147 5.11e+01 d.17.4.7 83567 1y97A 238 5.19e+01 c.55.3.5 122773 2dj5A 133 5.24e+01 c.92.1.3 131536 2gcoA 201 5.25e+01 1vc1A 110 5.25e+01 c.13.2.1 108493 3hzpA 131 5.27e+01 2cjaA 522 5.28e+01 1exqA 154 5.34e+01 1b9dA c.55.3.2 33646 2o1rA 81 5.35e+01 d.145.1.4 148549 3dclA 284 5.35e+01 1gvmA 136 5.35e+01 b.109.1.1 70612 1h0hA 977 5.37e+01 b.52.2.2,c.81.1.1 76435,76436 1yvuA 706 5.40e+01 b.34.14.1,c.55.3.10 124120,124121 1uv4A 293 5.45e+01 b.67.2.1 119705 3h8vA 292 5.49e+01 3kr9A 225 5.50e+01 1rwrA 301 5.51e+01 b.80.1.11 97990 2zxdA 455 5.54e+01 3ke7A 134 5.61e+01 3g12A 128 5.64e+01 3laeA 81 5.65e+01 2c3vA 102 5.70e+01 1ya0A 497 5.71e+01 a.118.8.1 122785 3eehA 125 5.72e+01 3l48A 94 5.72e+01 3jv1A 182 5.74e+01 3id4A 93 5.75e+01 2v2fF 390 5.82e+01 3hrzA 627 5.83e+01 3g6jA 644 5.89e+01 3mgdA 157 5.97e+01 2ns2A 242 6.02e+01 1pf5A 131 6.06e+01 d.79.1.1 94604 1oa8A 133 6.06e+01 b.145.1.1 92698 3eesA 153 6.09e+01 1vr4A 103 6.10e+01 d.230.5.1 120432 2w9qA 87 6.11e+01 2pd1A 104 6.16e+01 d.58.4.11 149387 2gr8A 99 6.17e+01 d.24.1.4 135522 2kkuA 161 6.18e+01 1hl9A 449 6.18e+01 b.71.1.3,c.1.8.11 90650,90651 1kq5A 159 6.19e+01 b.80.5.1 68795 2r4iA 123 6.20e+01 d.17.4.15 151576 3a9iA 376 6.25e+01 3cxgA 133 6.26e+01 1xtlA 175 6.26e+01 1h8gA 95 6.26e+01 b.109.1.1 65735 3fpqA 290 6.27e+01 2zh7A 436 6.27e+01 a.160.1.3,d.218.1.7,d.58.16.2 154451,154452,154453 3grnA 153 6.30e+01 2ra9A 150 6.33e+01 1r7lA 110 6.35e+01 d.277.1.1 104837 1xj4A 119 6.35e+01 d.110.3.2 122027 2re3A 194 6.36e+01 2bdwA 362 6.36e+01 2pn1A 331 6.38e+01 1waaA 93 6.46e+01 1s4iA 175 6.47e+01 1htrB 329 6.52e+01 1smrA 2o0uA 364 6.56e+01 d.144.1.7 138868 1skoB 130 6.59e+01 d.110.7.1 105677 2czrA 226 6.60e+01 c.52.4.1 146440 1kdkA 177 6.64e+01 b.29.1.4 72351 1b5fA 239 6.65e+01 1smrA b.50.1.2 26836 3k5rA 218 6.68e+01 1htwA 158 6.69e+01 c.37.1.18 71083 3fiaA 121 6.69e+01 1l1oC 181 6.70e+01 b.40.4.3 73480 2oc6A 124 6.70e+01 d.198.4.1 148721 1oixA 191 6.76e+01 c.37.1.8 118710 1w6sA 599 6.78e+01 b.70.1.1 114284 1oivA 191 6.80e+01 c.37.1.8 93076 3hr6A 436 6.81e+01 1jqsC 68 6.88e+01 i.1.1.1 63239 3elsA 158 6.89e+01 3ijfX 133 6.90e+01 2uyzB 79 6.92e+01 d.15.1.1 140039 1gyhA 318 6.96e+01 b.67.2.1 70757 2obdA 476 6.97e+01 2gzxA 265 6.98e+01 3lp9A 227 6.99e+01 1hp1A 516 7.04e+01 d.114.1.1,d.159.1.2 70976,70977 1bmqA 167 7.04e+01 1pauA c.17.1.1 30998 3gwiA 170 7.13e+01 2k8qA 134 7.13e+01 2h4uA 145 7.14e+01 d.38.1.5 136082 1o0wA 252 7.14e+01 a.149.1.1,d.50.1.1 80751,80752 3g7pA 156 7.15e+01 2vzkA 173 7.16e+01 2a74A 643 7.18e+01 2qziA 103 7.19e+01 1k52A 72 7.20e+01 d.15.7.1 68148 2p13A 90 7.22e+01 d.145.1.4 149152 1gskA 513 7.26e+01 b.6.1.3,b.6.1.3,b.6.1.3 83314,83315,83316 1m98A 317 7.29e+01 a.175.1.1,d.17.4.6 78866,78867 3k1uA 330 7.30e+01 1f5fA 205 7.37e+01 1d2sA b.29.1.4 24222 2ztjA 382 7.37e+01 3cpnA 330 7.37e+01 1gydB 315 7.39e+01 b.67.2.1 70751 3ip4B 483 7.39e+01 2wftA 458 7.41e+01 1tr9A 341 7.42e+01 c.1.8.7 112617 2iyfA 430 7.45e+01 2qt6A 498 7.45e+01 3kbqA 172 7.48e+01 1orrA 347 7.50e+01 c.2.1.2 93460 3f8kA 160 7.51e+01 2r3iA 298 7.52e+01 2ichA 335 7.52e+01 b.176.1.1 147602 3fpxA 499 7.53e+01 2wg3C 463 7.59e+01 1xodA 118 7.59e+01 b.55.1.4 122202 2wg5A 109 7.66e+01 2jkdA 187 7.67e+01 2zpmA 91 7.68e+01 1mzyA 333 7.68e+01 b.6.1.3,b.6.1.3 103848,103849 3hmiA 292 7.70e+01 2z84A 218 7.75e+01 2cy9A 140 7.77e+01 d.38.1.5 131019 1m41A 380 7.84e+01 c.1.16.4 78595 1ei1A 391 7.84e+01 1aj6 d.14.1.3,d.122.1.2 37570,41104 1yqdA 366 7.87e+01 3cfzA 292 7.91e+01 1ms9A 648 7.98e+01 b.29.1.15,b.68.1.1 85088,85089 2bhoA 130 7.98e+01